Starting phenix.real_space_refine (version: dev) on Mon Feb 27 20:15:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/02_2023/6jqm_9874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/02_2023/6jqm_9874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/02_2023/6jqm_9874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/02_2023/6jqm_9874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/02_2023/6jqm_9874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jqm_9874/02_2023/6jqm_9874_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 544": "NH1" <-> "NH2" Residue "E ARG 545": "NH1" <-> "NH2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "E PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 545": "NH1" <-> "NH2" Residue "F ARG 580": "NH1" <-> "NH2" Residue "F PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30936 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "C" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "D" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "E" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "F" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.90, per 1000 atoms: 0.55 Number of scatterers: 30936 At special positions: 0 Unit cell: (179.14, 174.9, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 18 15.00 O 5832 8.00 N 5466 7.00 C 19470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.25 Conformation dependent library (CDL) restraints added in 4.7 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 51 sheets defined 31.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 41 through 57 removed outlier: 3.506A pdb=" N ARG A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix Processing helix chain 'A' and resid 61 through 77 removed outlier: 3.503A pdb=" N LEU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.899A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 114 removed outlier: 3.677A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 removed outlier: 4.153A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 187 through 200 removed outlier: 4.397A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.529A pdb=" N MET A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.505A pdb=" N LEU A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.748A pdb=" N VAL A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 316 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 354 removed outlier: 3.586A pdb=" N LYS A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 removed outlier: 4.416A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.677A pdb=" N GLN A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.061A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.551A pdb=" N VAL A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 567 No H-bonds generated for 'chain 'A' and resid 564 through 567' Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.632A pdb=" N ALA A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 61 through 77 removed outlier: 3.565A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 removed outlier: 4.014A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 removed outlier: 3.975A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 173 removed outlier: 4.149A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 187 through 200 removed outlier: 4.418A pdb=" N SER B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.580A pdb=" N MET B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 274 through 292 removed outlier: 5.979A pdb=" N LYS B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.781A pdb=" N VAL B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 319 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN B 320 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 321 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 355 removed outlier: 3.636A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 removed outlier: 4.359A pdb=" N GLY B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 removed outlier: 3.618A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 503 through 509 removed outlier: 4.128A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 584 through 595 removed outlier: 3.643A pdb=" N ALA B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 removed outlier: 3.836A pdb=" N ALA C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Proline residue: C 54 - end of helix Processing helix chain 'C' and resid 61 through 77 removed outlier: 3.596A pdb=" N LEU C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.807A pdb=" N ALA C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 116 removed outlier: 3.808A pdb=" N VAL C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 removed outlier: 4.206A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 187 through 200 removed outlier: 4.399A pdb=" N SER C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.665A pdb=" N MET C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 274 through 292 removed outlier: 6.132A pdb=" N LYS C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.750A pdb=" N VAL C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN C 309 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER C 312 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 315 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 354 removed outlier: 3.519A pdb=" N LYS C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 352 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 432 through 442 removed outlier: 3.641A pdb=" N ARG C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 503 through 509 removed outlier: 4.015A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.608A pdb=" N VAL C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 584 through 595 removed outlier: 3.621A pdb=" N ALA C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 80 through 89 removed outlier: 4.036A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 117 removed outlier: 3.847A pdb=" N VAL D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 165 No H-bonds generated for 'chain 'D' and resid 162 through 165' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 187 through 200 removed outlier: 4.466A pdb=" N SER D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 234 through 240 removed outlier: 3.689A pdb=" N MET D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 274 through 292 removed outlier: 5.993A pdb=" N LYS D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA D 291 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 321 removed outlier: 3.766A pdb=" N VAL D 308 " --> pdb=" O GLN D 305 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN D 309 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 310 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 318 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 319 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 321 " --> pdb=" O ARG D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 354 removed outlier: 3.662A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 432 through 442 removed outlier: 3.644A pdb=" N ARG D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 503 through 509 removed outlier: 4.041A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 549 through 559 Processing helix chain 'D' and resid 564 through 567 No H-bonds generated for 'chain 'D' and resid 564 through 567' Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.510A pdb=" N ALA D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 573' Processing helix chain 'D' and resid 584 through 595 removed outlier: 3.555A pdb=" N ALA D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 61 through 77 removed outlier: 3.551A pdb=" N LEU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 89 removed outlier: 3.848A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 117 removed outlier: 3.686A pdb=" N VAL E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 173 removed outlier: 4.287A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 187 through 200 removed outlier: 4.382A pdb=" N SER E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.728A pdb=" N MET E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 292 removed outlier: 6.081A pdb=" N LYS E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA E 291 " --> pdb=" O MET E 287 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 319 removed outlier: 3.809A pdb=" N VAL E 308 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN E 309 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 312 " --> pdb=" O ASN E 309 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 313 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 354 removed outlier: 3.544A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 419 removed outlier: 4.397A pdb=" N GLY E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.794A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 503 through 509 removed outlier: 3.914A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' Processing helix chain 'E' and resid 549 through 559 Processing helix chain 'E' and resid 564 through 567 No H-bonds generated for 'chain 'E' and resid 564 through 567' Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.551A pdb=" N ALA E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 595 removed outlier: 3.714A pdb=" N ALA E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 50 Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 61 through 77 removed outlier: 3.576A pdb=" N LEU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.900A pdb=" N ALA F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 117 removed outlier: 3.868A pdb=" N VAL F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP F 99 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 165 removed outlier: 3.754A pdb=" N MET F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 187 through 200 removed outlier: 4.457A pdb=" N SER F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.830A pdb=" N MET F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 292 removed outlier: 6.066A pdb=" N LYS F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA F 291 " --> pdb=" O MET F 287 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 321 removed outlier: 3.733A pdb=" N VAL F 308 " --> pdb=" O GLN F 305 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN F 309 " --> pdb=" O ALA F 306 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA F 310 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 315 " --> pdb=" O SER F 312 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN F 320 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 321 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 354 removed outlier: 3.590A pdb=" N ILE F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 419 removed outlier: 4.314A pdb=" N GLY F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 442 removed outlier: 3.763A pdb=" N ARG F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 503 through 509 removed outlier: 4.071A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 559 Processing helix chain 'F' and resid 571 through 573 No H-bonds generated for 'chain 'F' and resid 571 through 573' Processing helix chain 'F' and resid 584 through 595 Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 139 through 146 Processing sheet with id= C, first strand: chain 'A' and resid 252 through 256 removed outlier: 7.472A pdb=" N HIS A 153 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 179 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 402 through 406 removed outlier: 5.970A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 428 Processing sheet with id= F, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.502A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 545 through 547 removed outlier: 3.541A pdb=" N ASP A 622 " --> pdb=" O MET A 547 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.663A pdb=" N TRP A 32 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 6 through 8 Processing sheet with id= J, first strand: chain 'B' and resid 139 through 146 Processing sheet with id= K, first strand: chain 'B' and resid 252 through 256 removed outlier: 7.602A pdb=" N HIS B 153 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE B 179 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 402 through 406 removed outlier: 5.961A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL B 303 " --> pdb=" O CYS B 263 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 425 through 428 Processing sheet with id= N, first strand: chain 'B' and resid 545 through 547 Processing sheet with id= O, first strand: chain 'B' and resid 665 through 673 removed outlier: 5.368A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.710A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 6 through 8 Processing sheet with id= R, first strand: chain 'C' and resid 139 through 146 Processing sheet with id= S, first strand: chain 'C' and resid 252 through 256 removed outlier: 7.609A pdb=" N HIS C 153 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 179 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 402 through 406 removed outlier: 5.997A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 425 through 428 Processing sheet with id= V, first strand: chain 'C' and resid 539 through 541 Processing sheet with id= W, first strand: chain 'C' and resid 545 through 547 removed outlier: 3.569A pdb=" N ASP C 622 " --> pdb=" O MET C 547 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 646 through 651 Processing sheet with id= Y, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.772A pdb=" N TRP C 32 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= AA, first strand: chain 'D' and resid 139 through 146 Processing sheet with id= AB, first strand: chain 'D' and resid 252 through 256 removed outlier: 7.441A pdb=" N HIS D 153 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D 179 " --> pdb=" O HIS D 153 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 402 through 406 removed outlier: 5.982A pdb=" N ASN D 261 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 301 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS D 263 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL D 303 " --> pdb=" O CYS D 263 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 425 through 428 removed outlier: 3.511A pdb=" N LEU D 427 " --> pdb=" O GLN D 450 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 545 through 547 Processing sheet with id= AF, first strand: chain 'D' and resid 625 through 627 Processing sheet with id= AG, first strand: chain 'D' and resid 646 through 651 Processing sheet with id= AH, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.623A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= AJ, first strand: chain 'E' and resid 139 through 146 Processing sheet with id= AK, first strand: chain 'E' and resid 252 through 256 removed outlier: 7.497A pdb=" N HIS E 153 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE E 179 " --> pdb=" O HIS E 153 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 402 through 406 removed outlier: 6.039A pdb=" N ASN E 261 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE E 301 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS E 263 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL E 303 " --> pdb=" O CYS E 263 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 425 through 428 Processing sheet with id= AN, first strand: chain 'E' and resid 539 through 541 Processing sheet with id= AO, first strand: chain 'E' and resid 545 through 547 Processing sheet with id= AP, first strand: chain 'E' and resid 646 through 651 Processing sheet with id= AQ, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.723A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 6 through 8 Processing sheet with id= AS, first strand: chain 'F' and resid 139 through 146 Processing sheet with id= AT, first strand: chain 'F' and resid 252 through 256 removed outlier: 7.509A pdb=" N HIS F 153 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE F 179 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 402 through 406 removed outlier: 5.976A pdb=" N ASN F 261 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE F 301 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS F 263 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL F 303 " --> pdb=" O CYS F 263 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 425 through 428 Processing sheet with id= AW, first strand: chain 'F' and resid 545 through 547 Processing sheet with id= AX, first strand: chain 'F' and resid 665 through 673 removed outlier: 5.443A pdb=" N ALA F 652 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS F 630 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU F 654 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU F 628 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE F 656 " --> pdb=" O VAL F 626 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL F 626 " --> pdb=" O PHE F 656 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.618A pdb=" N TRP F 32 " --> pdb=" O ILE F 22 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.84 Time building geometry restraints manager: 13.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9294 1.33 - 1.46: 6728 1.46 - 1.58: 15286 1.58 - 1.71: 18 1.71 - 1.83: 252 Bond restraints: 31578 Sorted by residual: bond pdb=" CA VAL B 648 " pdb=" CB VAL B 648 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.05e-02 9.07e+03 3.14e+00 bond pdb=" N THR D 634 " pdb=" CA THR D 634 " ideal model delta sigma weight residual 1.461 1.481 -0.020 1.38e-02 5.25e+03 2.18e+00 bond pdb=" CB ASN F 158 " pdb=" CG ASN F 158 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.18e+00 bond pdb=" N THR C 634 " pdb=" CA THR C 634 " ideal model delta sigma weight residual 1.461 1.480 -0.019 1.38e-02 5.25e+03 1.94e+00 bond pdb=" CA VAL C 648 " pdb=" CB VAL C 648 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.75e+00 ... (remaining 31573 not shown) Histogram of bond angle deviations from ideal: 96.36 - 103.91: 601 103.91 - 111.46: 13503 111.46 - 119.00: 12189 119.00 - 126.55: 16122 126.55 - 134.10: 503 Bond angle restraints: 42918 Sorted by residual: angle pdb=" C ASN B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 angle pdb=" C ASN E 606 " pdb=" N TYR E 607 " pdb=" CA TYR E 607 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" C ASN D 606 " pdb=" N TYR D 607 " pdb=" CA TYR D 607 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C ASN F 606 " pdb=" N TYR F 607 " pdb=" CA TYR F 607 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ASN C 606 " pdb=" N TYR C 607 " pdb=" CA TYR C 607 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 ... (remaining 42913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 18654 33.68 - 67.35: 172 67.35 - 101.03: 14 101.03 - 134.70: 1 134.70 - 168.38: 5 Dihedral angle restraints: 18846 sinusoidal: 7326 harmonic: 11520 Sorted by residual: dihedral pdb=" CA ASP E 522 " pdb=" C ASP E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASP C 522 " pdb=" C ASP C 522 " pdb=" N ARG C 523 " pdb=" CA ARG C 523 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP A 522 " pdb=" C ASP A 522 " pdb=" N ARG A 523 " pdb=" CA ARG A 523 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 18843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3041 0.042 - 0.083: 1294 0.083 - 0.125: 471 0.125 - 0.167: 69 0.167 - 0.209: 9 Chirality restraints: 4884 Sorted by residual: chirality pdb=" CA TYR C 607 " pdb=" N TYR C 607 " pdb=" C TYR C 607 " pdb=" CB TYR C 607 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TYR D 607 " pdb=" N TYR D 607 " pdb=" C TYR D 607 " pdb=" CB TYR D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA TYR F 607 " pdb=" N TYR F 607 " pdb=" C TYR F 607 " pdb=" CB TYR F 607 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4881 not shown) Planarity restraints: 5598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 124 " 0.019 2.00e-02 2.50e+03 1.75e-02 7.64e+00 pdb=" CG TRP B 124 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 124 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 124 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 124 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 124 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 124 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 124 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 124 " 0.019 2.00e-02 2.50e+03 1.60e-02 6.38e+00 pdb=" CG TRP F 124 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP F 124 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 124 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 124 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 124 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" CG TRP D 124 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 124 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 124 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 124 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 124 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 124 " 0.003 2.00e-02 2.50e+03 ... (remaining 5595 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9268 2.82 - 3.34: 27468 3.34 - 3.86: 53265 3.86 - 4.38: 61831 4.38 - 4.90: 108509 Nonbonded interactions: 260341 Sorted by model distance: nonbonded pdb=" OG1 THR D 270 " pdb=" OD1 ASP D 272 " model vdw 2.304 2.440 nonbonded pdb=" OG1 THR F 270 " pdb=" OD1 ASP F 272 " model vdw 2.304 2.440 nonbonded pdb=" OG1 THR B 270 " pdb=" OD1 ASP B 272 " model vdw 2.312 2.440 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASP A 272 " model vdw 2.314 2.440 nonbonded pdb=" OG SER E 36 " pdb=" O SER E 214 " model vdw 2.318 2.440 ... (remaining 260336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 19470 2.51 5 N 5466 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 18.000 Check model and map are aligned: 0.490 Process input model: 77.730 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 31578 Z= 0.348 Angle : 0.831 10.110 42918 Z= 0.443 Chirality : 0.051 0.209 4884 Planarity : 0.007 0.062 5598 Dihedral : 10.759 168.380 11442 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.10), residues: 4056 helix: -3.10 (0.09), residues: 1368 sheet: -3.36 (0.16), residues: 654 loop : -2.67 (0.11), residues: 2034 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 695 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 696 average time/residue: 0.5213 time to fit residues: 541.3984 Evaluate side-chains 314 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 3.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 8.9990 chunk 169 optimal weight: 0.2980 chunk 104 optimal weight: 0.4980 chunk 205 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 500 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS D 500 GLN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 HIS E 500 GLN ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN F 500 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 31578 Z= 0.385 Angle : 0.628 8.550 42918 Z= 0.324 Chirality : 0.045 0.154 4884 Planarity : 0.006 0.050 5598 Dihedral : 7.944 172.731 4392 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.12), residues: 4056 helix: -1.72 (0.13), residues: 1386 sheet: -3.17 (0.16), residues: 678 loop : -2.10 (0.12), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 334 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 35 residues processed: 380 average time/residue: 0.4817 time to fit residues: 284.5787 Evaluate side-chains 292 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 257 time to evaluate : 3.465 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2870 time to fit residues: 23.2588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 303 optimal weight: 0.0870 chunk 248 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 365 optimal weight: 0.3980 chunk 395 optimal weight: 3.9990 chunk 325 optimal weight: 0.8980 chunk 362 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 293 optimal weight: 0.0970 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN A 450 GLN A 500 GLN A 606 ASN B 409 GLN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 342 GLN C 384 GLN C 450 GLN D 158 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 GLN E 450 GLN F 158 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 31578 Z= 0.159 Angle : 0.529 8.139 42918 Z= 0.267 Chirality : 0.041 0.175 4884 Planarity : 0.004 0.041 5598 Dihedral : 7.567 169.744 4392 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.12), residues: 4056 helix: -1.15 (0.13), residues: 1428 sheet: -2.93 (0.17), residues: 696 loop : -1.81 (0.13), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 298 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 322 average time/residue: 0.4751 time to fit residues: 242.2388 Evaluate side-chains 267 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3413 time to fit residues: 14.1597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 0.0770 chunk 274 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 367 optimal weight: 0.7980 chunk 388 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 347 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN B 74 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 659 HIS F 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 31578 Z= 0.265 Angle : 0.542 7.933 42918 Z= 0.274 Chirality : 0.042 0.179 4884 Planarity : 0.004 0.038 5598 Dihedral : 7.451 170.375 4392 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.13), residues: 4056 helix: -0.76 (0.14), residues: 1392 sheet: -2.60 (0.18), residues: 660 loop : -1.67 (0.13), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 292 average time/residue: 0.4825 time to fit residues: 219.9955 Evaluate side-chains 258 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 246 time to evaluate : 3.616 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2986 time to fit residues: 11.6292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 289 optimal weight: 0.0050 chunk 160 optimal weight: 3.9990 chunk 331 optimal weight: 0.8980 chunk 268 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 HIS C 3 GLN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 31578 Z= 0.186 Angle : 0.505 8.369 42918 Z= 0.253 Chirality : 0.041 0.138 4884 Planarity : 0.004 0.038 5598 Dihedral : 7.206 166.910 4392 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.13), residues: 4056 helix: -0.34 (0.14), residues: 1392 sheet: -2.35 (0.18), residues: 660 loop : -1.50 (0.13), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 287 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 302 average time/residue: 0.4836 time to fit residues: 229.6963 Evaluate side-chains 258 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 251 time to evaluate : 3.674 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2960 time to fit residues: 9.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN D 450 GLN E 450 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.055 31578 Z= 0.528 Angle : 0.665 7.823 42918 Z= 0.337 Chirality : 0.047 0.211 4884 Planarity : 0.005 0.047 5598 Dihedral : 7.738 175.760 4392 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 4056 helix: -0.50 (0.14), residues: 1392 sheet: -2.74 (0.17), residues: 726 loop : -1.41 (0.14), residues: 1938 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 3.658 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 276 average time/residue: 0.5047 time to fit residues: 217.8085 Evaluate side-chains 247 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 3.642 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2856 time to fit residues: 15.1776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 284 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 327 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 387 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 31578 Z= 0.211 Angle : 0.528 9.176 42918 Z= 0.266 Chirality : 0.042 0.209 4884 Planarity : 0.004 0.053 5598 Dihedral : 7.436 173.686 4392 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 4056 helix: -0.13 (0.14), residues: 1386 sheet: -2.45 (0.18), residues: 684 loop : -1.34 (0.13), residues: 1986 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 256 time to evaluate : 3.827 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 268 average time/residue: 0.5203 time to fit residues: 216.0227 Evaluate side-chains 239 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 3.673 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4968 time to fit residues: 8.0161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 246 optimal weight: 2.9990 chunk 263 optimal weight: 0.6980 chunk 191 optimal weight: 0.0870 chunk 36 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 HIS E 392 HIS ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 31578 Z= 0.178 Angle : 0.510 9.082 42918 Z= 0.256 Chirality : 0.041 0.217 4884 Planarity : 0.004 0.048 5598 Dihedral : 7.238 171.400 4392 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 4056 helix: 0.08 (0.14), residues: 1398 sheet: -2.26 (0.19), residues: 684 loop : -1.21 (0.14), residues: 1974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 267 time to evaluate : 3.968 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 277 average time/residue: 0.4997 time to fit residues: 217.6199 Evaluate side-chains 240 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 233 time to evaluate : 3.525 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2901 time to fit residues: 8.7456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 1.9990 chunk 371 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 326 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 31578 Z= 0.295 Angle : 0.559 10.807 42918 Z= 0.279 Chirality : 0.043 0.216 4884 Planarity : 0.004 0.051 5598 Dihedral : 7.316 172.735 4392 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 4056 helix: 0.10 (0.14), residues: 1398 sheet: -2.37 (0.18), residues: 714 loop : -1.16 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 3.616 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 240 average time/residue: 0.5166 time to fit residues: 191.5491 Evaluate side-chains 232 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 3.268 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2601 time to fit residues: 5.4705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 5.9990 chunk 381 optimal weight: 0.0270 chunk 233 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 400 optimal weight: 0.9980 chunk 368 optimal weight: 0.8980 chunk 318 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 246 optimal weight: 0.0010 chunk 195 optimal weight: 0.9990 overall best weight: 0.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 31578 Z= 0.175 Angle : 0.520 11.206 42918 Z= 0.259 Chirality : 0.041 0.236 4884 Planarity : 0.004 0.044 5598 Dihedral : 7.130 169.496 4392 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4056 helix: 0.30 (0.14), residues: 1398 sheet: -2.12 (0.19), residues: 684 loop : -1.12 (0.14), residues: 1974 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 239 time to evaluate : 3.786 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 242 average time/residue: 0.5335 time to fit residues: 199.9539 Evaluate side-chains 232 residues out of total 3174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 3.464 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2706 time to fit residues: 5.4827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 1.9990 chunk 339 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 294 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 327 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089977 restraints weight = 42242.255| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.14 r_work: 0.2900 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 31578 Z= 0.212 Angle : 0.526 11.025 42918 Z= 0.261 Chirality : 0.042 0.248 4884 Planarity : 0.004 0.048 5598 Dihedral : 7.068 167.987 4392 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4056 helix: 0.36 (0.14), residues: 1398 sheet: -2.22 (0.18), residues: 714 loop : -1.04 (0.14), residues: 1944 =============================================================================== Job complete usr+sys time: 6184.07 seconds wall clock time: 114 minutes 18.10 seconds (6858.10 seconds total)